Chih-Ying Lin wrote:
HI
1.
type =>
do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc
secondary-structure.xvg
Select a group: 1
Selected 1: 'Protein'
Don't analyze Protein. Think about it - you're looking at mainchain hydrogen
bonds. Side chains and such don't matter for DSSP. Use the MainChain+H group
for analysis.
-Justin
There are 129 residues in your selected group
Opening library file /usr/local/gromacs/share/gromacs/top/ss.map
Reading frame 0 time 0.000
Back Off! I just backed up dd6S1IAF to ./#dd6S1IAF.1#
dd0JIeYC dd2n5lZ5 dd6Lt1VG ddCKhtbw ddH0Kx1A
ddH1OHJw ddH7I7Jq ddHu6YEP
.......... etc are created........
=> DSSP has been taking one hour to analyze the lysozyme and not finish
yet
=> there may something wrong ???
2. The path of the DSSP file is /usr/local/bin/DSSP.
Both dsspcmbi and dsspcmbi.exe are in the file /usr/local/bin/DSSP.
3. So, the last step i type the command in my .profile.
setenv dssp /usr/local/bin/DSSP
export dssp= /usr/local/bin/DSSP
export PATH=$PATH:$DSSP
Is it correct ?
Thank you
Lin
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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